rs888663

Variant names:

• chr19-18374112-G-T
• rs888663

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.836 in 152,078 control chromosomes in the GnomAD database, including 53,320 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (53320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127014 AN: 151960 Hom.: 53272 Cov.: 31

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.814

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.836 AC: 127118 AN: 152078 Hom.: 53320 Cov.: 31 AF XY: 0.837 AC XY: 62160 AN XY: 74306

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.808

Alfa AF: 0.808 Hom.: 100207

Bravo AF: 0.837

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.079
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs888663; hg19: chr19-18484922;